[10201] | 1 | On line biogeochemistry coarsening |
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| 2 | ================================== |
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| 3 | |
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| 4 | .. include:: .global.rst |
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| 5 | |
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| 6 | .. contents:: |
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| 7 | :local: |
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| 8 | |
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| 9 | .. role:: underline |
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| 10 | :class: underline |
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| 11 | |
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| 12 | ------------ |
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| 13 | Presentation |
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| 14 | ------------ |
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| 15 | |
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| 16 | A capacity of coarsening physics to force a BGC model coupled to NEMO has been developed. |
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| 17 | This capacity allow to run 'online' a BGC model coupled to OCE-SI3 with a lower resolution, |
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| 18 | to reduce the CPU cost of the BGC model, while preserving the effective resolution of the dynamics. |
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| 19 | |
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| 20 | A presentation is available [attachment:crs_wiki_1.1.pdf here], where the methodology is presented. |
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| 21 | |
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| 22 | ----------------------------------------------------- |
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| 23 | What is available and working for now in this version |
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| 24 | ----------------------------------------------------- |
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| 25 | |
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| 26 | [To be completed] |
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| 27 | |
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| 28 | ---------------------------------------------- |
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| 29 | Description of the successful validation tests |
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| 30 | ---------------------------------------------- |
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| 31 | |
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| 32 | [To be completed] |
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| 33 | |
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| 34 | ------------------------------------------------------------------ |
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| 35 | What is not working yet with on line coarsening of biogeochemistry |
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| 36 | ------------------------------------------------------------------ |
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| 37 | |
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| 38 | [To be completed] |
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| 39 | |
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| 40 | ''should include precise explanation on MPI decomposition problems too'' |
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| 41 | |
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| 42 | --------------------------------------------- |
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| 43 | How to set up and use on line biogeochemistry |
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| 44 | --------------------------------------------- |
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| 45 | |
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| 46 | :underline:`How to activate coarsening?` |
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| 47 | |
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| 48 | To activate the coarsening, ``key_crs`` should be added to list of CPP keys. |
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| 49 | This key will only activate the coarsening of dynamics. |
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| 50 | |
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| 51 | Some parameters are available in the namelist_cfg: |
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| 52 | |
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| 53 | .. code-block:: fortran |
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| 54 | |
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| 55 | ! passive tracer coarsened online simulations |
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| 56 | !----------------------------------------------------------------------- |
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| 57 | nn_factx = 3 ! Reduction factor of x-direction |
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| 58 | nn_facty = 3 ! Reduction factor of y-direction |
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| 59 | nn_msh_crs = 0 ! create (=1) a mesh file or not (=0) |
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| 60 | nn_crs_kz = 3 ! 0, volume-weighted MEAN of KZ |
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| 61 | ! 1, MAX of KZ |
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| 62 | ! 2, MIN of KZ |
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| 63 | ! 3, 10^(MEAN(LOG(KZ)) |
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| 64 | ! 4, MEDIANE of KZ |
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| 65 | ln_crs_wn = .false. ! wn coarsened (T) or computed using horizontal divergence ( F ) |
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| 66 | ! ! |
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| 67 | ln_crs_top = .true. !coarsening online for the bio |
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| 68 | / |
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| 69 | |
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| 70 | - Only ``nn_factx = 3`` is available and the coarsening only works for grids with a T-pivot point for |
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| 71 | the north-fold lateral boundary condition (ORCA025, ORCA12, ORCA36, ...). |
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| 72 | - ``nn_msh_crs = 1`` will activate the generation of the coarsened grid meshmask. |
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| 73 | - ``nn_crs_kz`` is the operator to coarsen the vertical mixing coefficient. |
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| 74 | - ``ln_crs_wn`` |
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| 75 | |
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| 76 | - when ``key_vvl`` is activated, this logical has no effect; |
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| 77 | the coarsened vertical velocities are computed using horizontal divergence. |
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| 78 | - when ``key_vvl`` is not activated, |
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| 79 | |
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| 80 | - coarsened vertical velocities are computed using horizontal divergence (``ln_crs_wn = .false.``) |
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| 81 | - or coarsened vertical velocities are computed with an average operator (``ln_crs_wn = .true.``) |
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| 82 | - ``ln_crs_top = .true.``: should be activated to run BCG model in coarsened space; |
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| 83 | so only works when ``key_top`` is in the cpp list and eventually ``key_pisces`` or ``key_my_trc``. |
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| 84 | |
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| 85 | :underline:`Choice of operator to coarsene KZ` |
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| 86 | |
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| 87 | A sensiblity test has been done with an Age tracer to compare the different operators. |
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| 88 | The 3 and 4 options seems to provide the best results. |
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| 89 | |
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| 90 | Some results can be found [xxx here] |
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| 91 | |
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| 92 | :underline:`Example of xml files to output coarsened variables with XIOS` |
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| 93 | |
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| 94 | In the [attachment:iodef.xml iodef.xml] file, a "nemo" context is defined and |
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| 95 | some variable defined in [attachment:file_def.xml file_def.xml] are writted on the ocean-dynamic grid. |
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| 96 | To write variables on the coarsened grid, and in particular the passive tracers, |
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| 97 | a "nemo_crs" context should be defined in [attachment:iodef.xml iodef.xml] and |
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| 98 | the associated variable are listed in [attachment:file_crs_def.xml file_crs_def.xml ]. |
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| 99 | |
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| 100 | :underline:`Passive tracers tracers initial conditions` |
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| 101 | |
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| 102 | When initial conditions are provided in NetCDF files, the field might be: |
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| 103 | |
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| 104 | - on the coarsened grid |
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| 105 | - or they can be on another grid and |
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| 106 | interpolated `on-the-fly <http://forge.ipsl.jussieu.fr/nemo/wiki/Users/SetupNewConfiguration/Weight-creator>`_. |
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| 107 | Example of namelist for PISCES : |
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| 108 | |
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| 109 | .. code-block:: fortran |
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| 110 | |
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| 111 | !----------------------------------------------------------------------- |
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| 112 | &namtrc_dta ! Initialisation from data input file |
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| 113 | !----------------------------------------------------------------------- |
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| 114 | ! |
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| 115 | sn_trcdta(1) = 'DIC_REG1' , -12 , 'DIC' , .false. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 116 | sn_trcdta(2) = 'ALK_REG1' , -12 , 'ALK' , .false. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 117 | sn_trcdta(3) = 'O2_REG1' , -1 , 'O2' , .true. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 118 | sn_trcdta(5) = 'PO4_REG1' , -1 , 'PO4' , .true. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 119 | sn_trcdta(7) = 'Si_REG1' , -1 , 'Si' , .true. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 120 | sn_trcdta(10) = 'DOC_REG1' , -12 , 'DOC' , .false. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 121 | sn_trcdta(14) = 'Fe_REG1' , -12 , 'Fe' , .false. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 122 | sn_trcdta(23) = 'NO3_REG1' , -1 , 'NO3' , .true. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 123 | rn_trfac(1) = 1.0e-06 ! multiplicative factor |
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| 124 | rn_trfac(2) = 1.0e-06 ! - - - - |
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| 125 | rn_trfac(3) = 44.6e-06 ! - - - - |
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| 126 | rn_trfac(5) = 122.0e-06 ! - - - - |
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| 127 | rn_trfac(7) = 1.0e-06 ! - - - - |
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| 128 | rn_trfac(10) = 1.0e-06 ! - - - - |
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| 129 | rn_trfac(14) = 1.0e-06 ! - - - - |
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| 130 | rn_trfac(23) = 7.6e-06 ! - - - - |
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| 131 | |
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| 132 | cn_dir = './' ! root directory for the location of the data files |
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| 133 | |
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| 134 | :underline:`PISCES forcing files` |
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| 135 | |
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| 136 | They might be on the coarsened grid. |
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| 137 | |
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| 138 | :underline:`Perspectives` |
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| 139 | |
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| 140 | For the future, a few options are on the table to implement coarsening for biogeochemistry in 4.0 and |
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| 141 | future releases. |
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| 142 | Those will be discussed in Autumn 2018 |
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